RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

Mukai, Takahito; Crnković, Ana; Umehara, Takuya; Ivanova, Natalia N.; Kyrpides, Nikos C.; Söll, Dieter; Harwood, ed., Caroline S.; Ibba, Michael; Whitman, William

doi:10.1128/mBio.00561-17

Title: RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

Journal Article · Wed Jul 05 00:00:00 EDT 2017 · mBio

DOI:https://doi.org/10.1128/mBio.00561-17· OSTI ID:1786910

Mukai, Takahito ^[1]; Crnković, Ana ^[1]; Umehara, Takuya ^[2]; Ivanova, Natalia N. ^[3]; Kyrpides, Nikos C. ^[3]; Söll, Dieter ^[4]; Harwood, ed., Caroline S.; Ibba, Michael; Whitman, William

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA, Department of Biological Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo, Japan
Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA, Department of Chemistry, Yale University, New Haven, Connecticut, USA

ABSTRACT The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA^Cysis first acylated with phosphoserine (Sep) byO-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA^Cysby Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN,Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“CandidatusParcubacteria” andChloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNA^Cysspecies with cysteinein vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS-SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea andChloroflexibacteria. We further discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.

View Journal Article

Cite

Export

Save

Research Organization:: Yale Univ., New Haven, CT (United States); Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division; Japan Society for the Promotion of Science (JSPS); National Institutes of Health (NIH)

Grant/Contract Number:: FG02-98ER20311; AC02-05CH11231; R01GM22854; R35GM122560

OSTI ID:: 1786910

Alternate ID(s):: OSTI ID: 1425739

Journal Information:: mBio, Journal Name: mBio Vol. 8 Journal Issue: 3; ISSN 2161-2129

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 19 works

Citation information provided by
Web of Science

References (93)

Emergence of the universal genetic code imprinted in an RNA record Hohn, M. J.; Park, H.-S.; O'Donoghue, P. Proceedings of the National Academy of Sciences, Vol. 103, Issue 48, p. 18095-18100 https://doi.org/10.1073/pnas.0608762103	journal	November 2006
Asgard archaea illuminate the origin of eukaryotic cellular complexity Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H. Nature, Vol. 541, Issue 7637 https://doi.org/10.1038/nature21031	journal	January 2017
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics Evans, P. N.; Parks, D. H.; Chadwick, G. L. Science, Vol. 350, Issue 6259 https://doi.org/10.1126/science.aac7745	journal	October 2015
Diversity and abundance ofBacteria andArchaea in the Bor Khlueng Hot Spring in Thailand Kanokratana, Pattanop; Chanapan, Supavadee; Pootanakit, Kusol Journal of Basic Microbiology, Vol. 44, Issue 6 https://doi.org/10.1002/jobm.200410388	journal	December 2004
Methanogenic burst in the end-Permian carbon cycle Rothman, D. H.; Fournier, G. P.; French, K. L. Proceedings of the National Academy of Sciences, Vol. 111, Issue 15 https://doi.org/10.1073/pnas.1318106111	journal	March 2014
Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California: Investigation of microbial ecology in hydrothermal sediments McKay, Luke; Klokman, Vincent W.; Mendlovitz, Howard P. Environmental Microbiology Reports, Vol. 8, Issue 1 https://doi.org/10.1111/1758-2229.12365	journal	January 2016
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
Erratum: Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches Lazar, Cassandre S.; Baker, Brett J.; Seitz, Kiley W. The ISME Journal, Vol. 11, Issue 4 https://doi.org/10.1038/ismej.2017.8	journal	March 2017
Ancient horizontal gene transfer and the last common ancestors Fournier, Gregory P.; Andam, Cheryl P.; Gogarten, Johann Peter BMC Evolutionary Biology, Vol. 15, Issue 1 https://doi.org/10.1186/s12862-015-0350-0	journal	April 2015
“Altiarchaeales”: Uncultivated Archaea from the Subsurface Probst, Alexander; Moissl-Eichinger, Christine Life, Vol. 5, Issue 2 https://doi.org/10.3390/life5021381	journal	May 2015
Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNA ^Cys synthesis Chen, Meirong; Nakazawa, Yuto; Kubo, Yume Acta Crystallographica Section F Structural Biology Communications, Vol. 72, Issue 7 https://doi.org/10.1107/S2053230X16009559	journal	June 2016
A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes Liu, Yuchen; Vinyard, David J.; Reesbeck, Megan E. Proceedings of the National Academy of Sciences, Vol. 113, Issue 45 https://doi.org/10.1073/pnas.1615732113	journal	October 2016
Zinc-mediated Amino Acid Discrimination in Cysteinyl-tRNA Synthetase Zhang, Chun-Mei; Christian, Thomas; Newberry, Kate J. Journal of Molecular Biology, Vol. 327, Issue 5 https://doi.org/10.1016/S0022-2836(03)00241-9	journal	April 2003
An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism Makino, Yuki; Sato, Takaaki; Kawamura, Hiroki Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13446	journal	November 2016
Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin Dowell, Frederick; Cardman, Zena; Dasarathy, Srishti Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00017	journal	January 2016
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO ₂ concentrations : Genomic resolution of a high-CO Probst, Alexander J.; Castelle, Cindy J.; Singh, Andrea Environmental Microbiology, Vol. 19, Issue 2 https://doi.org/10.1111/1462-2920.13362	journal	July 2016
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction Seitz, Kiley W.; Lazar, Cassandre S.; Hinrichs, Kai-Uwe The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.233	journal	January 2016
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria Baker, Brett J.; Lazar, Cassandre Sara; Teske, Andreas P. Microbiome, Vol. 3, Issue 1 https://doi.org/10.1186/s40168-015-0077-6	journal	April 2015
Identification of a multi-protein reductive dehalogenase complex in D ehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement : Respiratory reductive dehalogenase protein complex Kublik, Anja; Deobald, Darja; Hartwig, Stefanie Environmental Microbiology, Vol. 18, Issue 9 https://doi.org/10.1111/1462-2920.13200	journal	February 2016
Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales Bird, Jordan T.; Baker, Brett J.; Probst, Alexander J. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01221	journal	August 2016
Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette Borrel, Guillaume; Gaci, Nadia; Peyret, Pierre Archaea, Vol. 2014, p. 1-11 https://doi.org/10.1155/2014/374146	journal	January 2014
A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase Ticak, T.; Kountz, D. J.; Girosky, K. E. Proceedings of the National Academy of Sciences, Vol. 111, Issue 43 https://doi.org/10.1073/pnas.1409642111	journal	October 2014
Pyrrolysyl-tRNA synthetase–tRNA^Pyl structure reveals the molecular basis of orthogonality Nozawa, Kayo; O’Donoghue, Patrick; Gundllapalli, Sarath Nature, Vol. 457, Issue 7233, p. 1163-1167 https://doi.org/10.1038/nature07611	journal	December 2008
Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria Mukai, Takahito; Reynolds, Noah; Crnković, Ana Life, Vol. 7, Issue 1 https://doi.org/10.3390/life7010008	journal	February 2017
Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase Newberry, K. J. The EMBO Journal, Vol. 21, Issue 11 https://doi.org/10.1093/emboj/21.11.2778	journal	June 2002
Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages Durbin, Alan M.; Teske, Andreas Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00168	journal	January 2012
[3′-32P]-labeling tRNA with nucleotidyltransferase for assaying aminoacylation and peptide bond formation Ledoux, Sarah; Uhlenbeck, Olke C. Methods, Vol. 44, Issue 2 https://doi.org/10.1016/j.ymeth.2007.08.001	journal	February 2008
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea Baker, Brett J.; Saw, Jimmy H.; Lind, Anders E. Nature Microbiology, Vol. 1, Issue 3 https://doi.org/10.1038/nmicrobiol.2016.2	journal	February 2016
Facile Recoding of Selenocysteine in Nature Mukai, Takahito; Englert, Markus; Tripp, H. James Angewandte Chemie International Edition, Vol. 55, Issue 17, p. 5337-5341 https://doi.org/10.1002/anie.201511657	journal	March 2016
Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea Hussain, Tanweer; Kruparani, Shobha P.; Pal, Biswajit The EMBO Journal, Vol. 25, Issue 17 https://doi.org/10.1038/sj.emboj.7601278	journal	August 2006
RamA, a Protein Required for Reductive Activation of Corrinoid-dependent Methylamine Methyltransferase Reactions in Methanogenic Archaea Ferguson, Tsuneo; Soares, Jitesh A.; Lienard, Tanja Journal of Biological Chemistry, Vol. 284, Issue 4 https://doi.org/10.1074/jbc.M807392200	journal	November 2008
A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase Hao, B. Science, Vol. 296, Issue 5572 https://doi.org/10.1126/science.1069556	journal	May 2002
Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea Rother, Michael; Krzycki, Joseph A. Archaea, Vol. 2010 https://doi.org/10.1155/2010/453642	journal	January 2010
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building Gouy, M.; Guindon, S.; Gascuel, O. Molecular Biology and Evolution, Vol. 27, Issue 2 https://doi.org/10.1093/molbev/msp259	journal	October 2009
Persulfide Formation Mediates Cysteine and Homocysteine Biosynthesis in Methanosarcina acetivorans Rauch, Benjamin J.; Klimek, John; David, Larry Biochemistry, Vol. 56, Issue 8 https://doi.org/10.1021/acs.biochem.6b00931	journal	February 2017
Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface Probst, Alexander J.; Weinmaier, Thomas; Raymann, Kasie Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6497	journal	November 2014
The physiology and habitat of the last universal common ancestor Weiss, Madeline C.; Sousa, Filipa L.; Mrnjavac, Natalia Nature Microbiology, Vol. 1, Issue 9 https://doi.org/10.1038/nmicrobiol.2016.116	journal	July 2016
Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems Mariotti, Marco; Lobanov, Alexei V.; Manta, Bruno Molecular Biology and Evolution, Vol. 33, Issue 9 https://doi.org/10.1093/molbev/msw122	journal	July 2016
Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen Nobu, Masaru Konishi; Narihiro, Takashi; Kuroda, Kyohei The ISME Journal, Vol. 10, Issue 10 https://doi.org/10.1038/ismej.2016.33	journal	March 2016
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C. Current Biology, Vol. 25, Issue 6 https://doi.org/10.1016/j.cub.2015.01.014	journal	March 2015
Evolutionary profiles from the QR factorization of multiple sequence alignments Sethi, A.; O'Donoghue, P.; Luthey-Schulten, Z. Proceedings of the National Academy of Sciences, Vol. 102, Issue 11 https://doi.org/10.1073/pnas.0409715102	journal	March 2005
Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Cheng, Lei; Qiu, Tian-Lei; Yin, Xiao-Bo International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 12 https://doi.org/10.1099/ijs.0.65049-0	journal	December 2007
Comparison of archaeal and bacterial community structures in heavily oil-contaminated and pristine soils Liu, Ruyin; Zhang, Yu; Ding, Ran Journal of Bioscience and Bioengineering, Vol. 108, Issue 5 https://doi.org/10.1016/j.jbiosc.2009.05.010	journal	November 2009
Direct charging of tRNA_CUA with pyrrolysine in vitro and in vivo Blight, Sherry K.; Larue, Ross C.; Mahapatra, Anirban Nature, Vol. 431, Issue 7006, p. 333-335 https://doi.org/10.1038/nature02895	journal	August 2004
Linking Microbial Community Structure to S, N and Fe Biogeochemical Cycling in the Hot Springs at the Tengchong Geothermal Fields, Southwest China Li, Jiwei; Peng, Xiaotong; Zhang, Lixue Geomicrobiology Journal, Vol. 33, Issue 2 https://doi.org/10.1080/01490451.2015.1043165	journal	February 2016
Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea Liu, Y.; Nakamura, A.; Nakazawa, Y. Proceedings of the National Academy of Sciences, Vol. 111, Issue 29 https://doi.org/10.1073/pnas.1411267111	journal	July 2014
Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments Kubo, Kyoko; Lloyd, Karen G.; F. Biddle, Jennifer The ISME Journal, Vol. 6, Issue 10 https://doi.org/10.1038/ismej.2012.37	journal	May 2012
Redundant Synthesis of Cysteinyl-tRNA ^Cys in Methanosarcina mazei Hauenstein, Scott I.; Perona, John J. Journal of Biological Chemistry, Vol. 283, Issue 32 https://doi.org/10.1074/jbc.M801839200	journal	June 2008
Novel proteins for homocysteine biosynthesis in anaerobic microorganisms Rauch, Benjamin Julius; Gustafson, Andrew; Perona, John J. Molecular Microbiology, Vol. 94, Issue 6 https://doi.org/10.1111/mmi.12832	journal	November 2014
RNA-Dependent Cysteine Biosynthesis in Archaea Sauerwald, Anselm; Zhu, Wenhong; Major, Tiffany A. Science, Vol. 307, Issue 5717, p. 1969-1972 https://doi.org/10.1126/science.1108329	journal	March 2005
A freestanding proofreading domain is required for protein synthesis quality control in Archaea Korencic, D.; Ahel, I.; Schelert, J. Proceedings of the National Academy of Sciences, Vol. 101, Issue 28 https://doi.org/10.1073/pnas.0403926101	journal	July 2004
Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea Klipcan, Liron; Frenkel-Morgenstern, Milana; Safro, Mark G. Trends in Genetics, Vol. 24, Issue 2 https://doi.org/10.1016/j.tig.2007.11.007	journal	February 2008
The evolutionary history of Cys-tRNACys formation O'Donoghue, P.; Sethi, A.; Woese, C. R. Proceedings of the National Academy of Sciences, Vol. 102, Issue 52 https://doi.org/10.1073/pnas.0509617102	journal	December 2005
Unusual biology across a group comprising more than 15% of domain Bacteria Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C. Nature, Vol. 523, Issue 7559 https://doi.org/10.1038/nature14486	journal	June 2015
An aminoacyl-tRNA synthetase that specifically activates pyrrolysine Polycarpo, C.; Ambrogelly, A.; Berube, A. Proceedings of the National Academy of Sciences, Vol. 101, Issue 34, p. 12450-12454 https://doi.org/10.1073/pnas.0405362101	journal	August 2004
Structural basis for methyl-donor–dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD Ito, Takuhiro; Masuda, Isao; Yoshida, Ken-ichi Proceedings of the National Academy of Sciences, Vol. 112, Issue 31 https://doi.org/10.1073/pnas.1422981112	journal	July 2015
Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA Srinivasan, G. Science, Vol. 296, Issue 5572 https://doi.org/10.1126/science.1069588	journal	May 2002
Crystal structure of archaeal tRNA(m1G37)methyltransferase aTrm5 Goto-Ito, Sakurako; Ito, Takuhiro; Ishii, Ryohei Proteins: Structure, Function, and Bioinformatics, Vol. 72, Issue 4 https://doi.org/10.1002/prot.22019	journal	April 2008
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea Fukunaga, Ryuya; Yokoyama, Shigeyuki Nature Structural & Molecular Biology, Vol. 14, Issue 4, p. 272-279 https://doi.org/10.1038/nsmb1219	journal	March 2007
Biased gene transfer and its implications for the concept of lineage Andam, Cheryl P.; Gogarten, J. Peter Biology Direct, Vol. 6, Issue 1 https://doi.org/10.1186/1745-6150-6-47	journal	January 2011
Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein Rauch, Benjamin Julius; Perona, John J. Journal of Bacteriology, Vol. 198, Issue 14 https://doi.org/10.1128/JB.00141-16	journal	May 2016
A new view of the tree of life Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik Nature Microbiology, Vol. 1, Issue 5 https://doi.org/10.1038/nmicrobiol.2016.48	journal	April 2016
Carbon source-dependent expansion of the genetic code in bacteria Prat, L.; Heinemann, I. U.; Aerni, H. R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 51 https://doi.org/10.1073/pnas.1218613110	journal	November 2012
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group Meyerdierks, Anke; Kube, Michael; Kostadinov, Ivaylo Environmental Microbiology, Vol. 12, Issue 2 https://doi.org/10.1111/j.1462-2920.2009.02083.x	journal	February 2010
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro Molecular Biology and Evolution, Vol. 33, Issue 7 https://doi.org/10.1093/molbev/msw054	journal	March 2016
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Barns, S. M.; Delwiche, C. F.; Palmer, J. D. Proceedings of the National Academy of Sciences, Vol. 93, Issue 17 https://doi.org/10.1073/pnas.93.17.9188	journal	August 1996
Cysteinyl-tRNA formation: the last puzzle of aminoacyl-tRNA synthesis Li, Tong; Graham, David E.; Stathopoulos, Constantinos FEBS Letters, Vol. 462, Issue 3, p. 302-306 https://doi.org/10.1016/S0014-5793(99)01550-1	journal	November 1999
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota Vanwonterghem, Inka; Evans, Paul N.; Parks, Donovan H. Nature Microbiology, Vol. 1, Issue 12 https://doi.org/10.1038/nmicrobiol.2016.170	journal	October 2016
Molecular Evolution of Translin Superfamily Proteins Within the Genomes of Eubacteria, Archaea and Eukaryotes Gupta, Gagan D.; Kale, Avinash; Kumar, Vinay Journal of Molecular Evolution, Vol. 75, Issue 5-6 https://doi.org/10.1007/s00239-012-9534-z	journal	November 2012
Methanogenesis and the Wood–Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association Borrel, Guillaume; Adam, Panagiotis S.; Gribaldo, Simonetta Genome Biology and Evolution, Vol. 8, Issue 6 https://doi.org/10.1093/gbe/evw114	journal	May 2016
Complex archaea that bridge the gap between prokaryotes and eukaryotes Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L. Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14447	journal	May 2015
Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA^Cys Zhang, Chun-Mei; Liu, Cuiping; Slater, Simon Nature Structural & Molecular Biology, Vol. 15, Issue 5, p. 507-514 https://doi.org/10.1038/nsmb.1423	journal	April 2008
Crystal Structure of Methylornithine Synthase (PylB): Insights into the Pyrrolysine Biosynthesis Quitterer, Felix; List, Anja; Eisenreich, Wolfgang Angewandte Chemie International Edition, Vol. 51, Issue 6 https://doi.org/10.1002/anie.201106765	journal	November 2011
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Insights into the phylogeny and coding potential of microbial dark matter Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander Nature, Vol. 499, Issue 7459 https://doi.org/10.1038/nature12352	journal	July 2013
Diversity and Stratification of Archaea in a Hypersaline Microbial Mat Robertson, Charles E.; Spear, John R.; Harris, J. Kirk Applied and Environmental Microbiology, Vol. 75, Issue 7 https://doi.org/10.1128/AEM.01811-08	journal	December 2008
A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine Longstaff, David G.; Larue, Ross C.; Faust, Joseph E. Proceedings of the National Academy of Sciences, Vol. 104, Issue 3 https://doi.org/10.1073/pnas.0610294104	journal	January 2007
Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5 Christian, T.; Lahoud, G.; Liu, C. RNA, Vol. 16, Issue 12 https://doi.org/10.1261/rna.2376210	journal	October 2010
Catalytic Mechanism of Sep-tRNA:Cys-tRNA Synthase: Sulfur Transfer Is Mediated By Disulfide And Persulfide Liu, Yuchen; Dos Santos, Patricia C.; Zhu, Xiang Journal of Biological Chemistry, Vol. 287, Issue 8, p. 5426-5433 https://doi.org/10.1074/jbc.M111.313700	journal	December 2011
Methane production from coal by a single methanogen Mayumi, D.; Mochimaru, H.; Tamaki, H. Science, Vol. 354, Issue 6309 https://doi.org/10.1126/science.aaf8821	journal	October 2016
Environmental distribution of two widespread uncultured freshwater Euryarchaeota clades unveiled by specific primers and quantitative PCR: Quantitative distribution of uncultured Euryarchaeota Restrepo-Ortiz, Claudia X.; Casamayor, Emilio O. Environmental Microbiology Reports, Vol. 5, Issue 6 https://doi.org/10.1111/1758-2229.12088	journal	August 2013
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth Marcy, Y.; Ouverney, C.; Bik, E. M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 29, p. 11889-11894 https://doi.org/10.1073/pnas.0704662104	journal	July 2007
IMG/M: integrated genome and metagenome comparative data analysis system Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw929	journal	October 2016
Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea Mwirichia, Romano; Alam, Intikhab; Rashid, Mamoon Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep19181	journal	January 2016
Discovery of a novel methanogen prevalent in thawing permafrost Mondav, Rhiannon; Woodcroft, Ben J.; Kim, Eun-Hae Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4212	journal	February 2014
Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments He, Y.; Li, M.; Perumal, V. Nature Microbiology, Vol. 1, Issue 6 https://doi.org/10.1038/nmicrobiol.2016.35	journal	April 2016
RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria Wrighton, Kelly C.; Castelle, Cindy J.; Varaljay, Vanessa A. The ISME Journal, Vol. 10, Issue 11 https://doi.org/10.1038/ismej.2016.53	journal	May 2016
A new assay for tRNA aminoacylation kinetics Wolfson, Alexey D.; Pleiss, Jeffrey A.; Uhlenbeck, Olke C. RNA, Vol. 4, Issue 8 https://doi.org/10.1017/S1355838298980700	journal	August 1998
Structural Insights into the Second Step of RNA-dependent Cysteine Biosynthesis in Archaea: Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus Fukunaga, Ryuya; Yokoyama, Shigeyuki Journal of Molecular Biology, Vol. 370, Issue 1 https://doi.org/10.1016/j.jmb.2007.04.050	journal	June 2007
Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt Jungbluth, Sean P.; Bowers, Robert M.; Lin, Huei-Ting The ISME Journal, Vol. 10, Issue 8 https://doi.org/10.1038/ismej.2015.248	journal	February 2016
A tRNA-dependent cysteine biosynthesis enzyme recognizes the selenocysteine-specific tRNA in Escherichia coli Yuan, Jing; Hohn, Michael J.; Sherrer, R. Lynn FEBS Letters, Vol. 584, Issue 13 https://doi.org/10.1016/j.febslet.2010.05.028	journal	May 2010
New CRISPR–Cas systems from uncultivated microbes Burstein, David; Harrington, Lucas B.; Strutt, Steven C. Nature, Vol. 542, Issue 7640 https://doi.org/10.1038/nature21059	journal	December 2016
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes Saw, Jimmy H.; Spang, Anja; Zaremba-Niedzwiedzka, Katarzyna Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, Issue 1678 https://doi.org/10.1098/rstb.2014.0328	journal	September 2015

Similar Records

Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems

Journal Article · Mon Jan 03 00:00:00 EST 2022 · Frontiers in Genetics · OSTI ID:1786910

Mukai, Takahito; Amikura, Kazuaki; Fu, Xian; +2 more

A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes

Journal Article · Mon Oct 24 00:00:00 EDT 2016 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1786910

Liu, Yuchen; Vinyard, David J.; Reesbeck, Megan E.; +5 more

Toward Understanding Phosphoseryl-tRNA Cys Formation: The Crystal Structure of Methanococcus maripaludis Phosphoseryl-tRNA Synthetase

Journal Article · Mon Jan 01 00:00:00 EST 2007 · Proceedings of the National Academy of Sciences of the USA · OSTI ID:1786910

Kamtekar, S; Hohn, M; Park, h; +4 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
biochemistry
bioinformatics
cysteine biosynthesis
genetic code
translation

Title: RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

Citation Formats

References (93)

Similar Records

Related Subjects